scholarly journals Beyond fish eDNA metabarcoding: Field replicates disproportionately improve the detection of stream-associated vertebrate species

2021 ◽  
Vol 4 ◽  
Author(s):  
Till-Hendrik Macher ◽  
Robin Schütz ◽  
Jens Arle ◽  
Arne Beermann ◽  
Jan Koschorreck ◽  
...  
Keyword(s):  
Species Richness ◽  
Native Species ◽  
Bird Species ◽  
Sampling Strategy ◽  
Freshwater Ecosystems ◽  
Federal State ◽  
Vertebrate Species ◽  
Species Detection ◽  
Terrestrial Species ◽  
Biological Replication

Fast, reliable, and comprehensive biodiversity monitoring data are needed for environmental decision making and management. Recent work on fish environmental DNA (eDNA) metabarcoding shows that aquatic diversity can be captured fast, reliably, and non-invasively at moderate costs. Because freshwater ecosystems act as sinks in the landscape, they also collect traces of terrestrial species via surface runoff or when specimens come into direct contact with water (e.g., for drinking purposes). Thus, fish eDNA metabarcoding data can provide information on fish but also on other, even terrestrial vertebrate species that live in riparian habitats. This data become available and may offer a much more comprehensive approach for assessing vertebrate diversity at no additional costs. Studies on how the sampling strategy affects species detection especially of stream-associated communities, however, are scarce. We therefore performed an analysis on the effects of biological replication on both fish as well as (semi-)terrestrial species detection. Along a 2-km stretch of the river Mulde (Germany), we collected 18 1L water samples and analyzed the relation of detected species richness and quantity of biological replicates taken. We detected 58 vertebrate species, of which 25 were fish and lamprey, 18 mammals, and 15 birds, which account for 50%, 24% and 7% of all native species to the German federal state of Saxony-Anhalt. However, while increasing the number of biological replicates resulted in only 25 % more detected fish and lamprey species, mammal and bird species richness increased disproportionately by 69 % and 84 %, respectively. Contrary, PCR replicates showed little stochasticity. We thus emphasize to increase the number of biological replicates when the aim is to improve general species detections. This holds especially true, when the focus is on rare aquatic taxa or on (semi-)terrestrial species, the so-called ‘bycatch’. As a clear advantage, this information can be obtained without any additional sampling or laboratory effort when the sampling strategy regarding biological replication is chosen carefully. With the consideration of frequent eDNA metabarcoding as part of national biomonitoring programs, the additional information provided by the bycatch can be used to further investigate the state of the environment and its biodiversity on a much broader scale.

scholarly journals Beyond fish eDNA metabarcoding: Field replicates disproportionately improve the detection of stream associated vertebrate species

2021 ◽  
Vol 5 ◽  
Author(s):  
Till-Hendrik Macher ◽  
Robin Schütz ◽  
Jens Arle ◽  
Arne J. Beermann ◽  
Jan Koschorreck ◽  
...  
Keyword(s):  
Species Richness ◽  
Native Species ◽  
Bird Species ◽  
Sampling Strategy ◽  
Environmental Dna ◽  
Federal State ◽  
Vertebrate Species ◽  
Biodiversity Monitoring ◽  
Species Detection ◽  
Terrestrial Species

Fast, reliable, and comprehensive biodiversity monitoring data are needed for environmental decision making and management. Recent work on fish environmental DNA (eDNA) metabarcoding shows that aquatic diversity can be captured fast, reliably, and non-invasively at moderate costs. Because water in a catchment flows to the lowest point in the landscape, often a stream, it can collect traces of terrestrial species via surface or subsurface runoff along its way or when specimens come into direct contact with water (e.g., when drinking). Thus, fish eDNA metabarcoding data can provide information on fish but also on other vertebrate species that live in riparian habitats. This additional data may offer a much more comprehensive approach for assessing vertebrate diversity at no additional costs. Studies on how the sampling strategy affects species detection especially of stream-associated communities, however, are scarce. We therefore performed an analysis on the effects of biological replication on both fish as well as (semi-)terrestrial species detection. Along a 2 km stretch of the river Mulde (Germany), we collected 18 1-L water samples and analyzed the relation of detected species richness and quantity of biological replicates taken. We detected 58 vertebrate species, of which 25 were fish and lamprey, 18 mammals, and 15 birds, which account for 50%, 22.2%, and 7.4% of all native species to the German federal state of Saxony-Anhalt. However, while increasing the number of biological replicates resulted in only 24.8% more detected fish and lamprey species, mammal, and bird species richness increased disproportionately by 68.9% and 77.3%, respectively. Contrary, PCR replicates showed little stochasticity. We thus emphasize to increase the number of biological replicates when the aim is to improve general species detections. This holds especially true when the focus is on rare aquatic taxa or on (semi-)terrestrial species, the so-called ‘bycatch’. As a clear advantage, this information can be obtained without any additional sampling or laboratory effort when the sampling strategy is chosen carefully. With the increased use of eDNA metabarcoding as part of national fish bioassessment and monitoring programs, the complimentary information provided on bycatch can be used for biodiversity monitoring and conservation on a much broader scale.

scholarly journals Beyond fish eDNA metabarcoding: Field replicates disproportionately improve the detection of stream associated vertebrate species

2021 ◽  
Author(s):  
Till-Hendrik Macher ◽  
Robin Schuetz ◽  
Jens Arle ◽  
Arne J. Beermann ◽  
Jan Koschorreck ◽  
...  
Keyword(s):  
Species Richness ◽  
Native Species ◽  
Bird Species ◽  
Sampling Strategy ◽  
Environmental Dna ◽  
Federal State ◽  
Vertebrate Species ◽  
Biodiversity Monitoring ◽  
Species Detection ◽  
Terrestrial Species

Fast, reliable, and comprehensive biodiversity monitoring data are needed for environmental decision making and management. Recent work on fish environmental DNA (eDNA) metabarcoding shows that aquatic diversity can be captured fast, reliably, and non-invasively at moderate costs. Because water in a catchment flows to the lowest point in the landscape, often a stream, it can often collect traces of terrestrial species via surface or subsurface runoff along its way or when specimens come into direct contact with water (e.g., for drinking purposes). Thus, fish eDNA metabarcoding data can provide information on fish but also on other vertebrate species that live in riparian habitats. This additional data may offer a much more comprehensive approach for assessing vertebrate diversity at no additional costs. Studies on how the sampling strategy affects species detection especially of stream-associated communities, however, are scarce. We therefore performed an analysis on the effects of biological replication on both fish as well as (semi-)terrestrial species detection. Along a 2 km stretch of the river Mulde (Germany), we collected 18 1-L water samples and analyzed the relation of detected species richness and quantity of biological replicates taken. We detected 58 vertebrate species, of which 25 were fish and lamprey, 18 mammals, and 15 birds, which account for 50%, 24%, and 7% of all native species to the German federal state of Saxony-Anhalt. However, while increasing the number of biological replicates resulted in only 25% more detected fish and lamprey species, mammal, and bird species richness increased disproportionately by 69% and 84%, respectively. Contrary, PCR replicates showed little stochasticity. We thus emphasize to increase the number of biological replicates when the aim is to improve general species detections. This holds especially true, when the focus is on rare aquatic taxa or on (semi-)terrestrial species, the so-called 'bycatch'. As a clear advantage, this information can be obtained without any additional sampling or laboratory effort when the sampling strategy is chosen carefully. With the increased use of eDNA metabarcoding as part of national fish bioassessment and monitoring programs, the complimentary information provided on bycatch can be used for biodiversity monitoring and conservation on a much broader scale.

Impacts of Buffelgrass (Pennisetum ciliare) on a Forb Community in South Texas

2009 ◽  
Vol 2 (2) ◽  
pp. 130-140 ◽  
Author(s):  
Joseph P. Sands ◽  
Leonard A. Brennan ◽  
Fidel Hernández ◽  
William P. Kuvlesky ◽  
James F. Gallagher ◽  
...  
Keyword(s):  
Species Richness ◽  
Native Species ◽  
Grassland Birds ◽  
Bird Species ◽  
South Texas ◽  
Breeding Period ◽  
Stem Density ◽  
Grass Cover ◽  
Canopy Coverage ◽  
Useable Space

AbstractSince the 1950s, many south Texas rangelands have been seeded with buffelgrass, a perennial C4 bunchgrass native to Africa that is believed to contribute to reductions in biodiversity. Forb species represent a critical habitat component throughout the breeding period for many wildlife species as seed (summer to fall), as green vegetative material (spring to summer), and as habitat for arthropods (spring to summer). Reductions in richness and diversity of crucial ecosystem components such as forbs and arthropods have large implications for grassland birds and other wildlife. We sampled annual and perennial forbs within 1-m2 quadrats on 15 study plots (1 ha; n = 20 quadrats/plot) at Chaparral Wildlife Management Area, in LaSalle and Dimmit counties, Texas, during 2005 and 2006. Study plots were divided into five light-buffelgrass plots (0 to 5% buffelgrass canopy coverage), five moderate-buffelgrass plots (5 to 25% buffelgrass canopy coverage), and five heavy-buffelgrass plots (> 25% buffelgrass canopy coverage). Buffelgrass in study plots was composed of naturalized plants, and was not deliberately planted. During 2005 we observed that plots with > 25% buffelgrass had a 73% reduction in forb canopy of native species, a 64% reduction in native forb species richness, and a 77% reduction in native forb stem density compared to plots with 0 to 5% buffelgrass. These trends in native forb reduction (−79% native forb canopy, −65% forb species richness, −80% forb stem density) were nearly identical in 2006, even with greatly reduced rainfall. Simple linear regression revealed negative relationships between buffelgrass cover, total exotic grass cover (buffelgrass and Lehmann lovegrass), and total grass cover and the richness, coverage, and density of forbs/m2. Reductions in diversity may have larger implications regarding ecosystem function and available useable space and densities of desired bird species such as northern bobwhite.

Bushland modification and styles of urban development: their effects on birds in south-east Queensland

1998 ◽  
Vol 25 (1) ◽  
pp. 41 ◽  
Author(s):  
Sven R. Sewell ◽  
Carla P. Catterall
Keyword(s):  
Species Richness ◽  
Native Species ◽  
Bird Species ◽  
Individual Species ◽  
Bird Abundance ◽  
Bird Species Richness ◽  
Forest Clearing ◽  
Major Response ◽  
Forest Remnants ◽  
High Species Richness

Variation in bird assemblages associated with forest clearing and urbanisation in the greater Brisbane area was assessed by counting birds in sites within six habitat categories: large remnants, small remnants, no- understorey remnants, canopy suburbs (original trees present), planted suburbs, and bare suburbs. Total bird abundance and species richness were generally highest in canopy suburbs. Individual species showed many significant abundance differences among the habitat types, and were classified into three major response categories: bushland species (3 in summer, 13 in winter), tolerant species (13 in summer, 13 in winter), and suburban species (12 in summer, 11 in winter). The commonly proposed notion that urbanisation results in lowered bird species richness and increases in introduced species is broadly consistent with the observed differences between bare suburbs and large remnants. However, it does not adequately describe the situation in the planted and canopy suburbs, where there was high species richness and extremely high abundance of some native species (including noisy miners, lorikeets, friarbirds, and butcherbirds) but low abundance of a majority of the species common in the original habitats (including fantails, wrens, whistlers, and other small insectivores). Retained forest remnants are essential for the latter group. Urban plantings of prolifically flowering native species do not reverse the effects of deforestation, but promote a distinctive group of common native suburban bird species. Origins of the urban bird assemblage are discussed.

scholarly journals River Connectivity is Crucial for Safeguarding Biodiversity but May be Socially Overlooked. Insights From Spanish University Students

2021 ◽  
Vol 9 ◽  
Author(s):  
Elena Arboleya ◽  
Sara Fernández ◽  
Laura Clusa ◽  
Eduardo Dopico ◽  
Eva Garcia-Vazquez
Keyword(s):  
Species Richness ◽  
Functional Diversity ◽  
Native Species ◽  
Engineering Students ◽  
Educational Background ◽  
Freshwater Ecosystems ◽  
Fish Abundance ◽  
Fish Diversity ◽  
Nw Of Spain ◽  
Management Priorities

The social value of natural aquatic ecosystems is very important to set management priorities. River connectivity is essential for the conservation of freshwater ecosystems because barriers alter both abiotic conditions and the biotic communities, compromising biodiversity; however, the appreciation of this river feature has been insufficiently considered in socio-environmental studies that are mainly focused on the acceptance of new dams. Here we used a willingness to pay approach to estimate the value of connectivity, native species, fish diversity (measured as functional diversity or as species richness), fish abundance and environmental quality in three groups of students of different educational background in Asturias (NW of Spain). As in other studies where they are more sensitive to environmental issues, educational sciences students would pay more to conserve and improve river conditions than students of other disciplines. Connectivity was the least valued river feature by students of educational and natural sciences, and the third (before biodiversity and fish abundance) by engineering students. We measured the same features on lowland reaches of four coastal rivers in the Bay of Biscay, and applied declared will amounts to model their appreciation. Differences between the river ranks obtained from functional diversity (that changes with non-native species) and species richness, and small differences between students of different disciplines in the gap between most and least preferred rivers arise from the model. This indicates the importance to involve diverse stakeholder sectors in decisions about rivers. The importance of river connectivity in the conservation of local biodiversity should be explained to general public, perhaps through environmental campaigns.

Functional evenness of bird communities varies along the elevational gradient in Europe: Conservation implications

2019 ◽  
Author(s):  
Federico Morelli ◽  
Yanina
Keyword(s):  
Species Richness ◽  
Elevation Gradient ◽  
Bird Species ◽  
Elevational Gradient ◽  
Negative Association ◽  
Bird Communities ◽  
Breeding Bird ◽  
Bird Species Richness ◽  
Large Spatial Scale ◽  
Functional Evenness

ContextThe negative association between elevation and species richness is a well-recognized pattern in macro-ecology. ObjectivesThe aim of this study was to investigate changes in functional evenness of breeding bird communities along an elevation gradient in Europe. MethodsUsing the bird data from the EBCC Atlas of European Breeding Birds we estimated an index of functional evenness which can be assumed as a measure of the potential resilience of communities.ResultsOur findings confirm the existence of a negative association between elevation and bird species richness in all European eco regions. However, we also explored a novel aspect of this relationship, important for conservation: Our findings provide evidence at large spatial scale of a negative association between the functional evenness (potential community resilience) and elevation, independent of the eco region. We also found that the Natura2000 protected areas covers the territory most in need of protection, those characterized by bird communities with low potential resilience, in hilly and mountainous areas.ConclusionsThese results draw attention to European areas occupied by bird communities characterized by a potential lower capacity to respond to strong ecological changes, and, therefore, potentially more exposed to risks for conservation.

scholarly journals Patterns of bird species richness explained by annual variation in remotely sensed Dynamic Habitat Indices

2021 ◽  
Vol 127 ◽  
pp. 107774
Author(s):  
Martina L. Hobi ◽  
Laura S. Farwell ◽  
Maxim Dubinin ◽  
Dmitrij Kolesov ◽  
Anna M. Pidgeon ◽  
...  
Keyword(s):  
Species Richness ◽  
Annual Variation ◽  
Bird Species ◽  
Remotely Sensed ◽  
Bird Species Richness ◽  
Dynamic Habitat

scholarly journals Can clearcuts increase bird species richness in managed forests?

2008 ◽  
Vol 54 (No. 4) ◽  
pp. 189-193
Author(s):  
M. Żmihorski
Keyword(s):  
Species Richness ◽  
Bird Species ◽  
Bird Communities ◽  
Cumulative Number ◽  
Managed Forests ◽  
Managed Forest ◽  
Bird Species Richness ◽  
Forest Interior ◽  
Transect Counts ◽  
The Difference

Clearcuts are one of the results of forest management. The aim of this study was to assess the effect of clearcuts on bird communities in a managed forest in Western Poland. I applied the method of point transect counts. 20 points were located near clearcuts (less than 100 m from the nearest clearcut) and 25 points in the forest interior. In total, 36 bird species were recorded. On average, I found 9.20 bird species at points located near clearcuts and 6.72 species at points situated in the forest interior, and the difference was significant. The cumulative number of bird species for a given number of sampling points in the vicinity of clearcuts was higher than in the forest interior. The obtained results indicate that in managed, even-aged forests the generation of clearcuts can lead to an increase in local bird species richness.

Bird species richness and abundance in riparian vegetation invaded by exotic Reynoutria spp.

Biologia ◽  
2014 ◽  
Vol 69 (2) ◽  
Author(s):  
Lenka Hajzlerová ◽  
Jiří Reif
Keyword(s):  
Species Richness ◽  
Plant Species ◽  
Riparian Vegetation ◽  
Bird Species ◽  
Plant Invasions ◽  
Alien Plant ◽  
Bird Species Richness ◽  
River Bank ◽  
Management Actions ◽  
Acrocephalus Palustris

AbstractImpacts of invasive alien plant species are threatening biodiversity worldwide and thus it is important to assess their effects on particular groups of organisms. However, such impacts were studied mostly in case of plant or invertebrate communities and our understanding the response of vertebrate species to plant invasions remains incomplete. To improve our knowledge in this respect, we studied bird communities in riparian vegetation along the rivers with different levels of Reynoutria spp. invasion in the Czech Republic. These findings will be interesting for basic ecology enhancing our knowledge of consequences of plant invasions, as well as for conservation practice. We surveyed understory bird species in 26 vegetation blocks along parts of three rivers running from the Beskydy Mountains in spring 2011. We used principal component analysis to assess vegetation structure of particular blocks and the first axis ordinated the blocks according to the degree of invasion by Reynoutria spp. Using generalized linear mixed-effects models we found that counts of Motacilla cinerea, Cinclus cinclus and Sylvia borin, as well as the total bird species richness, significantly decreased with increasing degree of Reynoutria spp. invasion, while Acrocephalus palustris showed the opposite pattern. These results suggest that Reynoutria spp. impacts negatively on the species strictly bond with river banks and habitats specialists, whereas habitat generalist species like Sylvia atricapilla were not affected. Preference of Acrocephalus palustris for Reynoutria spp. corroborates affinity of this species to large invasive herbs observed also in other studies. Our study showed that Reynoutria spp. invasion can reduce species richness of understory birds in riparian communities. Although the distribution of this plant species is still quite limited in central Europe, our results suggest that its more widespread occurrence could potentially threat some river bank bird species. Therefore, we urge for development of management actions that will act counter the Reynoutria spp. invasion.

scholarly journals Modelling avian biodiversity using raw, unclassified satellite imagery

2014 ◽  
Vol 369 (1643) ◽  
pp. 20130197 ◽  
Author(s):  
Véronique St-Louis ◽  
Anna M. Pidgeon ◽  
Tobias Kuemmerle ◽  
Ruth Sonnenschein ◽  
Volker C. Radeloff ◽  
...  
Keyword(s):  
Species Richness ◽  
Habitat Heterogeneity ◽  
Bird Species ◽  
Image Texture ◽  
Spectral Mixture Analysis ◽  
Mixture Analysis ◽  
Bird Species Richness ◽  
Habitat Composition ◽  
Avian Biodiversity ◽  
Spectral Mixture

Applications of remote sensing for biodiversity conservation typically rely on image classifications that do not capture variability within coarse land cover classes. Here, we compare two measures derived from unclassified remotely sensed data, a measure of habitat heterogeneity and a measure of habitat composition, for explaining bird species richness and the spatial distribution of 10 species in a semi-arid landscape of New Mexico. We surveyed bird abundance from 1996 to 1998 at 42 plots located in the McGregor Range of Fort Bliss Army Reserve. Normalized Difference Vegetation Index values of two May 1997 Landsat scenes were the basis for among-pixel habitat heterogeneity (image texture), and we used the raw imagery to decompose each pixel into different habitat components (spectral mixture analysis). We used model averaging to relate measures of avian biodiversity to measures of image texture and spectral mixture analysis fractions. Measures of habitat heterogeneity, particularly angular second moment and standard deviation, provide higher explanatory power for bird species richness and the abundance of most species than measures of habitat composition. Using image texture, alone or in combination with other classified imagery-based approaches, for monitoring statuses and trends in biological diversity can greatly improve conservation efforts and habitat management.

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